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small changes here and there #105

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2 changes: 1 addition & 1 deletion tools/backsub/.shed.yml
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Expand Up @@ -3,7 +3,7 @@ name: backsub
description: "Background autofluorescence subtraction for MCMICRO"
long_description: |
"Pixel-by-pixel channel subtraction scaled by exposure times, primarily developed for images produced by the COMET platform and to work within the MCMICRO pipeline. Main usecase is autuofluorescence subtraction for multichannel and multicycle images for visualization of images from tissues with high autofluroescence (FFPE), improved segmentation, and quantification (if the previous two usecases aren't necessary, downstream subtraction of autofluorescent signal is encouraged as the script is memory inefficent)."
remote_repository_url: https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction
remote_repository_url: https://github.com/goeckslab/tools-mti/tree/main/tools/backsub
homepage_url: https://github.com/SchapiroLabor/Background_subtraction
categories:
- "Imaging"
2 changes: 1 addition & 1 deletion tools/mesmer/macros.xml
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Expand Up @@ -62,5 +62,5 @@
</xml>

<token name="@TOOL_VERSION@">0.12.3</token>
<token name="@VERSION_SUFFIX@">3</token>
<token name="@VERSION_SUFFIX@">4</token>
</macros>
29 changes: 20 additions & 9 deletions tools/mesmer/mesmer.xml
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Expand Up @@ -13,7 +13,7 @@
<expand macro="stdio"/>

<command detect_errors="exit_code"><![CDATA[
python $script
python '$script'
]]></command>
<configfiles>
<configfile name="script">
Expand Down Expand Up @@ -116,7 +116,7 @@ tifffile.imsave("mask.tif", mask)
</configfile>
</configfiles>
<inputs>
<param name="image" type="data" format="tiff, ome.tiff" label="Image containing the all marker(s)"/>
<param name="image" type="data" format="tiff,ome.tiff" label="Image containing the all marker(s)"/>
<param name="nuclear_channels" type="text" value="0" label="The numerical indices of the channel(s) for the nuclear markers" help="No quotes, separated by comma. e.g. 0, 1."/>
<param name="image_mpp" type="float" value="0.5" label="Resolution of the image in microns-per-pixel"/>
<param name="squeeze" type="boolean" checked="true" label="Whether to np.squeeze the outputs before saving"/>
Expand Down Expand Up @@ -153,7 +153,9 @@ tifffile.imsave("mask.tif", mask)
<tests>
<test expect_num_outputs="1">
<param name="image" value="deepcell_test.tiff" ftype="tiff"/>
<param name="compartment" value="nuclear" />
<conditional name="compartment_select">
<param name="compartment" value="nuclear" />
</conditional>
<param name="image_mpp" value="0.65" />
<param name="squeeze" value="True" />
<output name="mask" ftype="tiff">
Expand All @@ -164,9 +166,14 @@ tifffile.imsave("mask.tif", mask)
</test>
<test expect_num_outputs="1">
<param name="image" value="deepcell_test.tiff" ftype="tiff"/>
<param name="compartment" value="whole-cell" />
<param name="wc_channels" value="0, 1" />
<param name="maxima_threshold" value="0.075" />
<conditional name="compartment_select">
<param name="compartment" value="whole-cell" />
<section name="wc_options">
<param name="wc_channels" value="0, 1" />
<param name="maxima_threshold" value="0.075" />
</section>
</conditional>

<param name="image_mpp" value="0.65" />
<param name="squeeze" value="True" />
<output name="mask" ftype="tiff">
Expand All @@ -177,10 +184,14 @@ tifffile.imsave("mask.tif", mask)
</test>
<test expect_num_outputs="2">
<param name="image" value="deepcell_test.tiff" ftype="tiff"/>
<param name="compartment" value="both" />
<param name="image_mpp" value="0.65" />
<param name="wc_channels" value="1" />
<conditional name="compartment_select">
<param name="compartment" value="both" />
<section name="wc_options">
<param name="wc_channels" value="1" />
</section>
</conditional>
<param name="nuclear_channels" value="0" />
<param name="image_mpp" value="0.65" />
<param name="squeeze" value="True" />
<output name="wc_mask" ftype="tiff">
<assert_contents>
Expand Down
1 change: 0 additions & 1 deletion tools/scimap/scimap_spatial.xml
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Expand Up @@ -3,7 +3,6 @@
<macros>
<import>main_macros.xml</import>
</macros>

<expand macro="scimap_requirements"/>
<expand macro="macro_stdio" />
<version_command>echo "@VERSION@"</version_command>
Expand Down
34 changes: 23 additions & 11 deletions tools/squidpy/squidpy_spatial.xml
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Expand Up @@ -252,7 +252,9 @@
<tests>
<test expect_num_outputs="1">
<param name="anndata" value="imc.h5ad" ftype="h5ad" />
<param name="selected_tool" value="spatial_neighbors" />
<conditional name="analyses">
<param name="selected_tool" value="spatial_neighbors" />
</conditional>
<output name="output">
<assert_contents>
<has_h5_keys keys="uns/spatial_neighbors" />
Expand All @@ -261,8 +263,10 @@
</test>
<test expect_num_outputs="2">
<param name="anndata" value="imc_sn.h5ad" ftype="h5ad" />
<param name="selected_tool" value="nhood_enrichment" />
<param name="cluster_key" value="cell type" />
<conditional name="analyses">
<param name="selected_tool" value="nhood_enrichment" />
<param name="cluster_key" value="cell type" />
</conditional>
<output name="output">
<assert_contents>
<has_h5_keys keys="uns/cell type_nhood_enrichment" />
Expand All @@ -272,8 +276,10 @@
</test>
<test expect_num_outputs="2">
<param name="anndata" value="imc_sn.h5ad" ftype="h5ad" />
<param name="selected_tool" value="co_occurrence" />
<param name="cluster_key" value="cell type" />
<conditional name="analyses">
<param name="selected_tool" value="co_occurrence" />
<param name="cluster_key" value="cell type" />
</conditional>
<output name="output">
<assert_contents>
<has_h5_keys keys="uns/cell type_co_occurrence" />
Expand All @@ -283,8 +289,10 @@
</test>
<test expect_num_outputs="2">
<param name="anndata" value="imc_sn.h5ad" ftype="h5ad" />
<param name="selected_tool" value="centrality_scores" />
<param name="cluster_key" value="cell type" />
<conditional name="analyses">
<param name="selected_tool" value="centrality_scores" />
<param name="cluster_key" value="cell type" />
</conditional>
<output name="output">
<assert_contents>
<has_h5_keys keys="uns/cell type_centrality_scores" />
Expand All @@ -294,8 +302,10 @@
</test>
<test expect_num_outputs="2">
<param name="anndata" value="imc_sn.h5ad" ftype="h5ad" />
<param name="selected_tool" value="interaction_matrix" />
<param name="cluster_key" value="cell type" />
<conditional name="analyses">
<param name="selected_tool" value="interaction_matrix" />
<param name="cluster_key" value="cell type" />
</conditional>
<output name="output">
<assert_contents>
<has_h5_keys keys="uns/cell type_interactions" />
Expand All @@ -305,8 +315,10 @@
</test>
<test expect_num_outputs="2">
<param name="anndata" value="imc_sn.h5ad" ftype="h5ad" />
<param name="selected_tool" value="ripley" />
<param name="cluster_key" value="cell type" />
<conditional name="analyses">
<param name="selected_tool" value="ripley" />
<param name="cluster_key" value="cell type" />
</conditional>
<output name="output">
<assert_contents>
<has_h5_keys keys="uns/cell type_ripley_F" />
Expand Down
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